Thanks for your help Carlos and Jason. I think you are correct in that it may be easiest just to melt it.
Cheers,
brad
-----Original Message-----
From: Jason Swails [mailto:jason.swails.gmail.com]
Sent: Friday, October 29, 2010 10:39 AM
To: AMBER Mailing List
Subject: Re: [AMBER] Targeted MD - minimization problem
On the bright side, your restraint energy looks right.
Try visualizing your system using VMD or something (actually use the prmtop
file so the bonding information used by amber is loaded into the
visualizer). With numbers that bad you are certain to see something
violently wrong.
Good luck!
Jason
On Fri, Oct 29, 2010 at 11:36 AM, Carlos Simmerling <
carlos.simmerling.gmail.com> wrote:
> your initial energies are huge. how did you generate that input structure?
> bond energies should not be that large, and vdw is "not a number".
>
>
> On Fri, Oct 29, 2010 at 12:33 PM, Jordan, Brad <jbjordan.amgen.com> wrote:
>
> > Hi all - I'm attempting to fold a 160 residue protein from an extended
> > strand structure towards a final structure (the target) using targeted
> MD. I
> > have distance constraints that can be applied to do this. However, in my
> > initial minimization step, I get LINMIN failure as below. Here are both
> my
> > input file and the output file. Can anyone tell me what's going on? Any
> help
> > is greatly appreciated.
> >
> > Thanks,
> >
> > Brad
> >
> > Minimize.in
> >
> > Stage 1 - minimisation of extended strand
> > &cntrl
> > imin=1, maxcyc=1000, ncyc=500,
> > cut=999., igb=1, ntb=0,
> > ntpr=100,
> > &end
> >
> >
> >
> >
> > Output:
> >
> >
> > Here is the input file:
> >
> > Stage 1 - minimisation of TC5b
> > &cntrl
> > imin=1, maxcyc=1000, ncyc=500,
> > cut=99999., igb=1, ntb=0,
> > ntpr=100,
> > &end
> >
> >
> >
> --------------------------------------------------------------------------------
> > 1. RESOURCE USE:
> >
> >
> --------------------------------------------------------------------------------
> >
> > | Flags:
> > | New format PARM file being parsed.
> > | Version = 1.000 Date = 10/28/10 Time = 09:28:41
> > NATOM = 2634 NTYPES = 14 NBONH = 1337 MBONA = 1322
> > NTHETH = 3040 MTHETA = 1792 NPHIH = 5646 MPHIA = 3355
> > NHPARM = 0 NPARM = 0 NNB = 14598 NRES = 166
> > NBONA = 1322 NTHETA = 1792 NPHIA = 3355 NUMBND = 42
> > NUMANG = 89 NPTRA = 41 NATYP = 27 NPHB = 0
> > IFBOX = 0 NMXRS = 25 IFCAP = 0 NEXTRA = 0
> >
> >
> > | Memory Use Allocated Used
> > | Real 20000000 97664
> > | Hollerith 400000 15972
> > | Integer 60000000 135769
> > | Duplicated 0 dihedrals
> > | Duplicated 0 dihedrals
> >
> >
> >
> --------------------------------------------------------------------------------
> > 2. CONTROL DATA FOR THE RUN
> >
> >
> --------------------------------------------------------------------------------
> >
> >
> >
> > General flags:
> > imin = 1, nmropt = 0
> >
> > Nature and format of input:
> > ntx = 1, irest = 0, ntrx = 1
> >
> > Nature and format of output:
> > ntxo = 1, ntpr = 100, ntrx = 1, ntwr =
> > 500
> > iwrap = 0, ntwx = 0, ntwv = 0, ntwe =
> > 0
> > ioutfm = 0, ntwprt = 0, idecomp = 0, rbornstat=
> > 0
> >
> > Potential function:
> > ntf = 1, ntb = 0, igb = 1, nsnb =
> > 25
> > ipol = 0, gbsa = 0
> > dielc = 1.00000, cut =**********, intdiel = 1.00000
> > saltcon = 0.00000, offset = 0.09000, gbalpha= 1.00000
> > gbbeta = 0.00000, gbgamma = 0.00000, surften = 0.00500
> > scnb = 2.00000, scee = 1.20000
> >
> > Frozen or restrained atoms:
> > ibelly = 0, ntr = 0
> >
> > Energy minimization:
> > maxcyc = 1000, ncyc = 500, ntmin = 1
> > dx0 = 0.01000, dxm = 0.50000, drms = 0.00010
> >
> >
> >
> --------------------------------------------------------------------------------
> > 3. ATOMIC COORDINATES AND VELOCITIES
> >
> >
> --------------------------------------------------------------------------------
> >
> >
> > begin time read from input coords = 0.000 ps
> >
> > Number of triangulated 3-point waters found: 0
> >
> >
> >
> --------------------------------------------------------------------------------
> > 4. RESULTS
> >
> >
> --------------------------------------------------------------------------------
> >
> >
> >
> > NSTEP ENERGY RMS GMAX NAME NUMBER
> > 1 NAN NAN 0.0000E+00 N 1
> >
> > BOND = 18948008.4414 ANGLE = 432.7759 DIHED =
> > 1486.5571
> > VDWAALS = ************* EEL = -26859.4121 EGB =
> > nan
> > 1-4 VDW = 1985.1114 1-4 EEL = 6622.9339 RESTRAINT =
> > 0.0000
> >
> >
> > NSTEP ENERGY RMS GMAX NAME NUMBER
> > 100 NAN NAN 0.0000E+00 N 1
> >
> > BOND = nan ANGLE = nan DIHED =
> > 747.7200
> > VDWAALS = nan EEL = nan EGB =
> > nan
> > 1-4 VDW = nan 1-4 EEL = nan RESTRAINT =
> > 0.0000
> >
> >
> > NSTEP ENERGY RMS GMAX NAME NUMBER
> > 200 NAN NAN 0.0000E+00 N 1
> >
> > BOND = nan ANGLE = nan DIHED =
> > 747.7200
> > VDWAALS = nan EEL = nan EGB =
> > nan
> > 1-4 VDW = nan 1-4 EEL = nan RESTRAINT =
> > 0.0000
> >
> >
> > NSTEP ENERGY RMS GMAX NAME NUMBER
> > 300 NAN NAN 0.0000E+00 N 1
> >
> > BOND = nan ANGLE = nan DIHED =
> > 747.7200
> > VDWAALS = nan EEL = nan EGB =
> > nan
> > 1-4 VDW = nan 1-4 EEL = nan RESTRAINT =
> > 0.0000
> >
> >
> > NSTEP ENERGY RMS GMAX NAME NUMBER
> > 400 NAN NAN 0.0000E+00 N 1
> >
> > BOND = nan ANGLE = nan DIHED =
> > 747.7200
> > VDWAALS = nan EEL = nan EGB =
> > nan
> > 1-4 VDW = nan 1-4 EEL = nan RESTRAINT =
> > 0.0000
> >
> >
> > NSTEP ENERGY RMS GMAX NAME NUMBER
> > 500 NAN NAN 0.0000E+00 N 1
> >
> > BOND = nan ANGLE = nan DIHED =
> > 747.7200
> > VDWAALS = nan EEL = nan EGB =
> > nan
> > 1-4 VDW = nan 1-4 EEL = nan RESTRAINT =
> > 0.0000
> >
> > .... RESTARTED DUE TO LINMIN FAILURE ...
> >
> > .... RESTARTED DUE TO LINMIN FAILURE ...
> >
> > .... RESTARTED DUE TO LINMIN FAILURE ...
> >
> > .... RESTARTED DUE TO LINMIN FAILURE ...
> >
> > .... RESTARTED DUE TO LINMIN FAILURE ...
> >
> >
> > FINAL RESULTS
> >
> >
> >
> > NSTEP ENERGY RMS GMAX NAME NUMBER
> > 521 NAN NAN 0.0000E+00 N 1
> >
> > BOND = nan ANGLE = nan DIHED =
> > 747.7200
> > VDWAALS = nan EEL = nan EGB =
> > nan
> > 1-4 VDW = nan 1-4 EEL = nan RESTRAINT =
> > 0.0000
> >
> > ***** REPEATED LINMIN FAILURE *****
> >
> >
> >
> --------------------------------------------------------------------------------
> > 5. TIMINGS
> >
> >
> --------------------------------------------------------------------------------
> >
> >
> > | Highest rstack allocated: 28974
> > | Highest istack allocated: 5268
> >
> > | Setup wallclock 1 seconds
> > | Nonsetup wallclock 283 seconds
> >
> >
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Wed Nov 03 2010 - 11:30:03 PDT
